aquaduct.traj.sandwich module¶

class Window(start, stop, step)[source]¶

Bases: object

__init__(start, stop, step)[source]¶

__repr__()[source]¶

range()[source]¶

get_real(frame)[source]¶

len()[source]¶

class MasterReader[source]¶

Bases: object

open_reader_traj = {}¶

topology = ''¶

trajectory = ['']¶

window = None¶

sandwich_mode = None¶

engine_name = 'mda'¶

__call__(topology, trajectory, window=None, sandwich=False)[source]¶

Parameters:	topology (str) – Topology file name. trajectory (list) – List of trajectories. Each element is a fine name. window (Window) – Frames window to read. sandwich (bool) – Flag for setting sandwitch mode.

__getstate__()[source]¶

__setstate__(state)[source]¶

engine¶

correct_window()[source]¶

__repr__()[source]¶

sandwich(number=False)[source]¶

baguette(number=False)[source]¶

iterate(number=False)[source]¶

get_single_reader(number)[source]¶

get_reader_by_id(someid)[source]¶

real_number_of_frames()[source]¶

number_of_frames(onelayer=False)[source]¶

number_of_layers()[source]¶

class ReaderAccess[source]¶

Bases: object

reader¶

VdW_radii = {'ge': 2.11, 'gd': 2.34, 'ga': 1.87, 'la': 2.43, 'li': 1.82, 'tl': 1.96, 'lu': 2.24, 'lr': 2.46, 'th': 2.45, 'ti': 2.11, 'te': 2.06, 'tb': 2.33, 'tc': 2.16, 'ta': 2.22, 'yb': 2.26, 'dy': 2.31, 'xe': 2.16, 'h': 1.1, 'p': 1.8, 'tm': 2.27, 'zn': 2.01, 'eu': 2.35, 'es': 2.45, 'er': 2.29, 'ru': 2.13, 're': 2.16, 'ra': 2.83, 'rb': 3.03, 'rn': 2.2, 'rh': 2.1, 'be': 1.53, 'ba': 2.68, 'bi': 2.07, 'bk': 2.44, 'br': 1.85, 'c': 1.7, 'k': 2.75, 'o': 1.52, 's': 1.8, 'w': 2.18, 'os': 2.16, 'co': 2.0, 'cm': 2.45, 'cl': 1.75, 'ca': 2.31, 'cf': 2.45, 'ce': 2.42, 'cd': 2.18, 'cs': 3.43, 'cr': 2.06, 'cu': 1.96, 'pr': 2.4, 'pt': 2.13, 'pu': 2.43, 'pb': 2.02, 'pa': 2.43, 'pd': 2.1, 'po': 1.97, 'pm': 2.38, 'ho': 2.3, 'hf': 2.23, 'hg': 2.23, 'he': 1.4, 'md': 2.46, 'mg': 1.73, 'b': 1.92, 'f': 1.47, 'mo': 2.17, 'mn': 2.05, 'n': 1.55, 'v': 2.07, 'ac': 2.47, 'ag': 2.11, 'ir': 2.13, 'am': 2.44, 'al': 1.84, 'as': 1.85, 'ar': 1.88, 'au': 2.14, 'at': 2.02, 'in': 1.93, 'ni': 1.97, 'no': 2.46, 'na': 2.27, 'nb': 2.18, 'nd': 2.39, 'ne': 1.54, 'zr': 2.23, 'np': 2.39, 'fr': 3.48, 'y': 2.32, 'fe': 2.04, 'fm': 2.45, 'i': 1.98, 'sr': 2.49, 'kr': 2.02, 'si': 2.1, 'u': 2.41, 'sn': 2.17, 'sm': 2.36, 'sc': 2.15, 'sb': 2.06, 'se': 1.9}¶

Dictionary of VdW radii.

Data taken from L. M. Mentel, mendeleev, 2014. Available at: https://bitbucket.org/lukaszmentel/mendeleev. Package mendeleev is not used because it depends on too many other libraries.

class ReaderTraj(topology, trajectory, number=None, window=None)[source]¶

Bases: aquaduct.traj.sandwich.ReaderAccess

__init__(topology, trajectory, number=None, window=None)[source]¶

Parameters:	topology (str) – Topology file name. trajectory (list) – Trajectory file name. number (int) – Number of trajectory file. window (Window) – Frames window to read. reader (Reader) – Parent reader object.